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changeset: 158:15ded9e606d0
tag: tip
user: ajamesonpratt
date: Tue Jul 29 16:33:27 2014 -0400
files: plothist.py
description:
Added ability to overlay contour plot to plothist
changeset: 157:35d162ab49a5
user: joshua.adelman <[email protected]>
date: Wed Oct 02 09:28:25 2013 -0500
files: w_assign.py
description:
Fixed bug #44: w_assign produces error when using RecursiveMapper
changeset: 156:35d78507d873
user: Nick Rego <[email protected]>
date: Tue Sep 24 13:22:17 2013 -0400
files: w_eddist.py
description:
another push
changeset: 155:1e42d29b58ae
user: Nick Rego <[email protected]>
date: Tue Sep 24 13:15:29 2013 -0400
files: w_eddist.py
description:
change to dsspec class in eddist
changeset: 154:0aa0d92895c8
user: Nick Rego <[email protected]>
date: Tue Sep 24 12:46:25 2013 -0400
files: w_eddist.py
description:
progress indicator for w_eddist
changeset: 153:f231701a1304
user: Nick Rego <[email protected]>
date: Tue Sep 24 12:11:00 2013 -0400
files: w_eddist.py
description:
added preliminary event duration distribution tool (used like w_pdist)
changeset: 152:fdf4abbcaa1f
user: joshua.adelman <[email protected]>
date: Tue Sep 10 11:03:46 2013 -0400
files: w_kinavg.py
description:
Fixed bug in w_kinavg in which the conditional flux evolution results were not being recorded to the .h5 file correctly
changeset: 151:ae471188f0ae
user: joshua.adelman <[email protected]>
date: Wed Sep 04 15:43:20 2013 -0500
files: w_kinavg.py
description:
Added ability to define a fractional window in cumulative evolution mode for w_kinavg
changeset: 150:cb5a02777f5e
user: ajamesonpratt
date: Wed Jul 31 15:53:48 2013 -0400
files: w_kinetics.py westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx
description:
Adjusted kinetics scripts (w_kinetics.py and _kinetics.pyx) to dump seg_id in kinetics.h5
changeset: 149:c560ee88d258
user: Matt Zwier <[email protected]>
date: Thu Jul 18 21:05:46 2013 -0400
files: plothist.py w_pdist.py westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx
description:
Added pairwise factoring for multistate rate calculations.
changeset: 148:48cc8fa48068
user: Matt Zwier <[email protected]>
date: Sat Jul 06 13:31:37 2013 -0400
files: w_assign.py w_kinetics.py w_ntop.py w_select.py westpa/binning/__init__.py westpa/binning/_assign.c westpa/binning/_assign.pyx westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx westpa/kinetics/matrates.py
description:
Added w_ntop to select segments from bins.
Modified w_select to include weights for convenience.
Modified w_kinetics to support post-hoc analysis with unlabeled rate matrices.
changeset: 147:e4704bb9b396
parent: 146:0a6c07c2e68c
parent: 145:cc3d6394acdd
user: Matt Zwier <[email protected]>
date: Wed Jun 26 07:54:22 2013 -0400
description:
Merging cc3d6394acdd and 0a6c07c2e68c
changeset: 146:0a6c07c2e68c
parent: 144:7304d3bffe5e
user: Matt Zwier <[email protected]>
date: Tue Jun 25 15:41:43 2013 -0400
files: fasthist/__init__.py fasthist/__main__.py fasthist/_fasthist.c fasthist/_fasthist.pyx w_pdist.py westtools/core.py
description:
Added support for simply skipping points that are out of range in fasthist
(and thus w_pdist), handy for conditional probability distribution plots.
Fixed Heisenbug in multidimensional histograms in fasthist, which may have had
impact on the very first bin (in C order) of multidimensional histogram
results.
changeset: 145:cc3d6394acdd
user: joshua.adelman <[email protected]>
date: Fri Jun 21 09:31:05 2013 -0400
files: tests/testkinetics.py westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx westpa/kinetics/rate_averaging.py
description:
Changed algorithm for calculating accumulating statistics in _kinetics.pyx to improve numerical stability
changeset: 144:7304d3bffe5e
user: Matt Zwier <[email protected]>
date: Wed Jun 19 20:20:20 2013 -0400
files: w_crawl.py
description:
Removed outdated arg processing in w_crawl
changeset: 143:34c596cd2b64
user: Matt Zwier <[email protected]>
date: Wed Jun 12 17:20:29 2013 -0400
files: w_kinetics.py westpa/binning/assign.py
description:
Fixed performance regression in RecursiveBinMapper, added warning that w_kinetics matrix is experimental.
changeset: 142:421a04bb5d5e
parent: 141:86d7659599a8
parent: 138:ccef54debee0
user: Matt Zwier <[email protected]>
date: Wed Jun 12 15:53:02 2013 -0400
files: functional_tests/t_treewalker.py w_assign.py w_crawl.py w_pdist.py w_select.py w_stateprobs.py westtools/core.py westtools/tool_classes/__init__.py westtools/tool_classes/binning.py westtools/tool_classes/core.py westtools/tool_classes/data_reader.py westtools/tool_classes/iter_range.py westtools/tool_classes/progress.py westtools/tool_classes/selected_segs.py westtools/trajlib/__init__.py westtools/trajlib/trajtree.py westtools/trajlib/treewalker.py
description:
Merging ccef54debee0 and 86d7659599a8
changeset: 141:86d7659599a8
user: Matt Zwier <[email protected]>
date: Wed Jun 12 15:52:30 2013 -0400
files: w_assign.py w_crawl.py w_pdist.py w_select.py w_stateprobs.py westtools/tool_classes/core.py
description:
Changed all parallel tools to use submit_as_completed() instead of submit() to control RAM use. Activate by using --max-queue-length.
changeset: 140:425f93b95363
parent: 139:9a31a6449b63
parent: 135:79f9259d02d0
user: Matt Zwier <[email protected]>
date: Fri Jun 07 16:50:20 2013 -0400
description:
Merging 9a31a6449b63 and 79f9259d02d0
changeset: 139:9a31a6449b63
parent: 134:b9aab7ed36a3
user: Matt Zwier <[email protected]>
date: Wed Jun 05 16:07:14 2013 -0400
files: w_assign.py
description:
Minor modification to w_assign to support ZMQ work manager in dedicated
server mode.
changeset: 138:ccef54debee0
user: Matt Zwier <[email protected]>
date: Wed Jun 12 15:44:47 2013 -0400
files: functional_tests/t_treewalker.py ploterr.py plothist.py w_assign.py w_bins.py w_crawl.py w_dumpsegs.py w_fluxanl.py w_kinavg.py w_kinetics.py w_pdist.py w_select.py w_stateprobs.py w_trace.py westtools/__init__.py westtools/binning.py westtools/core.py westtools/data_reader.py westtools/iter_range.py westtools/progress.py westtools/selected_segs.py westtools/tool_classes/__init__.py westtools/tool_classes/binning.py westtools/tool_classes/core.py westtools/tool_classes/data_reader.py westtools/tool_classes/iter_range.py westtools/tool_classes/progress.py westtools/tool_classes/selected_segs.py westtools/trajlib/__init__.py westtools/trajlib/trajtree.py westtools/trajlib/treewalker.py
description:
Eliminated largely dead treewalker, eliminated west_tools package.
changeset: 137:2b065bebfeed
parent: 136:b95d61a6458d
parent: 135:79f9259d02d0
user: Matt Zwier <[email protected]>
date: Wed Jun 12 12:31:17 2013 -0400
description:
Merging b95d61a6458d and 79f9259d02d0
changeset: 136:b95d61a6458d
parent: 134:b9aab7ed36a3
user: Matt Zwier <[email protected]>
date: Wed Jun 12 12:30:05 2013 -0400
files: tests/testbinning.py westpa/binning/assign.py
description:
Fixed incorrect use of list vs dict in RecursiveBinMapper. Added unit test for
regression testing. Fixes #37.
changeset: 135:79f9259d02d0
user: Nick Rego <[email protected]>
date: Thu Jun 06 14:48:23 2013 -0400
files: plothist.py
description:
Fixed minor plothist bug - plotting in instant mode no longer always plots the last iteration
changeset: 134:b9aab7ed36a3
parent: 133:adff73e44247
parent: 132:6df9a9dca29c
user: Matt Zwier <[email protected]>
date: Wed Jun 05 16:05:38 2013 -0400
description:
Merging adff73e44247 and 6df9a9dca29c
changeset: 133:adff73e44247
parent: 129:1cb220dc4fff
user: Matt Zwier <[email protected]>
date: Wed Jun 05 16:05:04 2013 -0400
files: w_assign.py w_kinavg.py w_kinetics.py westpa/binning/_assign.c westpa/binning/_assign.pyx westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx westpa/kinetics/matrates.py westtools/tool_classes/data_reader.py
description:
Added option to suppress steady state population extrapolations in w_kinavg.
Modifications to support kinetics analysis on ancient (WEMD) HDF5 files.
changeset: 132:6df9a9dca29c
parent: 131:aa0fc2b62916
parent: 130:dd8f3bf65d14
user: Nick Rego <[email protected]>
date: Wed Jun 05 14:32:53 2013 -0400
description:
merge
changeset: 131:aa0fc2b62916
parent: 122:93c8bb04cc79
user: Nick Rego <[email protected]>
date: Wed Jun 05 14:30:19 2013 -0400
files: westpa/h5io.py
description:
Fixed h5io bug in SingleSegDSSPEC's get_iter_data() method
changeset: 130:dd8f3bf65d14
user: joshua.adelman <[email protected]>
date: Mon Jun 03 16:33:41 2013 -0400
files: w_trace.py
description:
Fixed bug in parsing dataset options in w_trace
changeset: 129:1cb220dc4fff
user: joshua.adelman <[email protected]>
date: Thu May 23 16:53:33 2013 -0400
files: tests/testkinetics.py westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx westpa/kinetics/rate_averaging.py
description:
Bug fix addressing issue #34 and issue #35; Uses new online statistics algorithm
to calculate mean and variance of flux and rate matrices, reducing the memory footprint of the calculation and fixing
error in rate calculation for transiently occupied bins
changeset: 128:dc717b762bb2
user: Adam P <[email protected]>
date: Mon May 20 15:38:46 2013 -0400
files: plothist.py
description:
Fix for the instant 2d plotting mechanism of plothist
changeset: 127:910b2178af83
user: Matt Zwier <[email protected]>
date: Mon May 20 11:49:10 2013 -0400
files: plothist.py
description:
Added plot postprocess hook to plothist.py
changeset: 126:c7d224b93c0e
user: Matt Zwier <[email protected]>
date: Sat May 11 09:52:00 2013 -0400
files: w_crawl.py westpa/progress.py
description:
Added try...finally wrapping for w_crawl that calls finalize(), modified
progress.py so that the cursor is only hidden in fancy mode.
changeset: 125:42130aee6e83
user: Matt Zwier <[email protected]>
date: Fri May 10 22:46:03 2013 -0400
files: w_crawl.py
description:
Added w_crawl, a simple general task coordinator for WESTPA data.
changeset: 124:4437d61e988a
user: Matt Zwier <[email protected]>
date: Thu May 09 14:47:21 2013 -0400
files: w_select.py w_stateprobs.py
description:
Retooled w_select
changeset: 123:d45f3ae13f1b
user: Matt Zwier <[email protected]>
date: Mon May 06 15:04:56 2013 -0400
files: w_kinetics.py westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx
description:
Modified trace routines to return number of transitions and w_kinetics to store.
changeset: 122:93c8bb04cc79
user: Matt Zwier <[email protected]>
date: Mon May 06 14:12:02 2013 -0400
files: fasthist/__init__.py westpa/h5io.py
description:
Corrected normalization for non-uniform bin widths in fasthist. Fixed UnboundLocal error in h5io.py.
changeset: 121:22ff2d89408f
user: Matt Zwier <[email protected]>
date: Wed May 01 10:22:13 2013 -0400
files: plothist.py westpa/progress.py
description:
Tweaks
changeset: 120:4add8a7ff4ea
user: Matt Zwier <[email protected]>
date: Mon Apr 29 13:59:03 2013 -0400
files: w_assign.py w_fluxanl.py w_kinavg.py w_kinetics.py westtools/tool_classes/binning.py westtools/tool_classes/progress.py
description:
Added support to w_assign to get bins from a YAML file.
Added support to w_kinetics and w_kinavg to report state-to-state fluxes as
well as rates.
changeset: 119:5a869b584954
user: Matt Zwier <[email protected]>
date: Wed Apr 24 17:31:47 2013 -0400
files: fasthist/_fasthist.c mclib/_mclib.c trajtree/_trajtree.c westpa/binning/_assign.c westpa/kinetics/_kinetics.c
description:
Forced update of Cython files to fix mysterious inconsistency in _kinetics.c
changeset: 118:fff3c8352980
user: Matt Zwier <[email protected]>
date: Wed Apr 24 17:09:54 2013 -0400
files: ploterr.py w_assign.py w_stateprobs.py westpa/binning/__init__.py westpa/binning/_assign.c westpa/binning/_assign.pyx westpa/h5io.py westpa/progress.py
description:
Added ``w_stateprobs`` tool (and corresponding plot mode to ``ploterr``) to
calculate block-bootstrapped macrostate populations (replaces ``w_binprobs``).
changeset: 117:4fadcccf43b8
user: Matt Zwier <[email protected]>
date: Wed Apr 24 11:22:56 2013 -0400
files: ploterr.py w_fluxanl.py w_kinavg.py westpa/h5io.py westpa/progress.py westtools/dtypes.py westtools/tool_classes/progress.py
description:
Added new "ploterr" script to plot output of w_kinavg --evolution-mode.
changeset: 116:a7e32a67b47d
parent: 113:ee3d0c0dd326
parent: 115:ced62ac1c742
user: Matt Zwier <[email protected]>
date: Tue Apr 23 16:59:03 2013 -0400
files: w_pcpdist.py
description:
Merging
changeset: 115:ced62ac1c742
parent: 111:bd2fa43abeda
parent: 114:f08402c430fd
user: Matt Zwier <[email protected]>
date: Tue Apr 23 13:58:03 2013 -0400
files: w_fluxanl.py w_kinavg.py w_kinetics.py w_pcpdist.py w_pdist.py w_select.py westpa/h5io.py westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx westpa/progress.py westtools/tool_classes/progress.py
description:
Merging
changeset: 114:f08402c430fd
parent: 106:afa4fb2e193e
user: Matt Zwier <[email protected]>
date: Sat Apr 20 21:46:27 2013 -0400
files: w_fluxanl.py w_kinavg.py w_kinetics.py w_pcpdist.py w_pdist.py w_select.py westpa/h5io.py westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx westpa/progress.py westtools/tool_classes/progress.py
description:
Updates to use progress bar
changeset: 113:ee3d0c0dd326
user: Matt Zwier <[email protected]>
date: Tue Apr 23 16:57:37 2013 -0400
files: westtools/__init__.py
description:
Removed dangling UsesMCBS import
changeset: 112:96214e0f019c
user: Matt Zwier <[email protected]>
date: Tue Apr 23 14:37:13 2013 -0400
files: westpa/binning/_assign.c westpa/binning/_assign.pyx
description:
Reverted changes to _assign.pyx, changed to numpy buffer protocol
changeset: 111:bd2fa43abeda
user: Matt Zwier <[email protected]>
date: Tue Apr 23 13:33:36 2013 -0400
files: fasthist/_fasthist.c mclib/_mclib.c trajtree/_trajtree.c westpa/binning/_assign.c westpa/binning/_assign.pyx westpa/kinetics/_kinetics.c
description:
Coerce slices to numpy arrays in apply_down and apply_down_argmin_across in _assign.pyx
changeset: 110:9b29827dc104
user: Matt Zwier <[email protected]>
date: Tue Apr 23 11:54:05 2013 -0400
files: fasthist/__init__.py fasthist/_fasthist.pyx mclib/__init__.py mclib/_mclib.pyx plothist.py setup.py tests/testbinning.py trajtree/_trajtree.pyx trajtree/trajtree.py w_assign.py w_bins.py w_dumpsegs.py w_fluxanl.py w_kinavg.py w_kinetics.py w_pcpdist.py w_pdist.py w_select.py w_trace.py westpa/_rc.py westpa/binning/_assign.pyx westpa/binning/assign.py westpa/binning/bins.py westpa/extloader.py westpa/h5io.py westpa/kinetics/_kinetics.pyx westpa/kinetics/matrates.py westpa/kinetics/rate_averaging.py westpa/progress.py westpa/textio.py westpa/yamlcfg.py westtools/tool_classes/binning.py westtools/tool_classes/core.py westtools/tool_classes/data_reader.py westtools/tool_classes/iter_range.py westtools/tool_classes/progress.py westtools/tool_classes/selected_segs.py westtools/trajlib/trajtree.py westtools/trajlib/treewalker.py
description:
Updated copyright information
changeset: 109:184b83ddf79f
user: Matt Zwier <[email protected]>
date: Sat Apr 20 21:47:23 2013 -0400
files: westpa/progress.py westtools/tool_classes/progress.py
description:
Adding progress bar license info
changeset: 108:113d1a9943a6
parent: 107:c36ec7f9130f
parent: 106:afa4fb2e193e
user: Matt Zwier <[email protected]>
date: Sat Apr 20 21:45:04 2013 -0400
files: plothist.py tests/testwtools.py w_assign.py w_pdist.py westpa/kinetics/matrates.py westtools/tool_classes/__init__.py westtools/tool_classes/core.py
description:
Merging
changeset: 107:c36ec7f9130f
parent: 101:67495d11610c
user: Matt Zwier <[email protected]>
date: Sat Apr 20 21:43:25 2013 -0400
files: fasthist/__init__.py fasthist/_fasthist.pyx mclib/__init__.py mclib/_mclib.pyx plothist.py setup.py tests/testbinning.py tests/testwtools.py trajtree/_trajtree.pyx trajtree/trajtree.py w_assign.py w_bins.py w_dumpsegs.py w_fluxanl.py w_kinavg.py w_kinetics.py w_pcpdist.py w_pdist.py w_select.py w_trace.py westpa/__init__.py westpa/_rc.py westpa/binning/_assign.pyx westpa/binning/assign.py westpa/binning/bins.py westpa/extloader.py westpa/h5io.py westpa/kinetics/_kinetics.pyx westpa/kinetics/matrates.py westpa/kinetics/rate_averaging.py westpa/plugins.py westpa/textio.py westpa/yamlcfg.py westtools/__init__.py westtools/stats/__init__.py westtools/stats/edfs.py westtools/stats/mcbs.py westtools/tool_classes/__init__.py westtools/tool_classes/binning.py westtools/tool_classes/core.py westtools/tool_classes/data_reader.py westtools/tool_classes/iter_range.py westtools/tool_classes/selected_segs.py westtools/tool_classes/stats.py westtools/trajlib/trajtree.py westtools/trajlib/treewalker.py
description:
Added copyright and license info. General cleanup.
Source files are (c) individual contributors; package is (c) MCZ and LTC.
changeset: 106:afa4fb2e193e
user: Matt Zwier <[email protected]>
date: Wed Apr 17 13:03:03 2013 -0400
files: w_assign.py w_pdist.py westpa/progress.py westtools/tool_classes/__init__.py westtools/tool_classes/progress.py
description:
Added support for progress bars (requires ``blessings`` library)
changeset: 105:18cc62e18713
user: Matt Zwier <[email protected]>
date: Tue Apr 16 19:32:32 2013 -0400
files: plothist.py w_pdist.py westtools/tool_classes/core.py
description:
Updated plothist to use subcommand framework, added a check in subcommands
framework for forgetting to set the "subcommand" class variable on subcommand
classes.
changeset: 104:28573311dd68
parent: 103:3d7148cbde7b
parent: 102:28626a2923d0
user: Matt Zwier <[email protected]>
date: Tue Apr 16 07:40:12 2013 -0400
files: tests/testwtools.py
description:
Merging
changeset: 103:3d7148cbde7b
parent: 101:67495d11610c
user: Matt Zwier <[email protected]>
date: Tue Apr 16 07:39:05 2013 -0400
files: westpa/kinetics/matrates.py
description:
Revert an untested change to sink handling.
changeset: 102:28626a2923d0
user: Nick Rego <[email protected]>
date: Mon Apr 15 17:15:54 2013 -0400
files: tests/testwtools.py tool_tests/__init__.py tool_tests/common.py tool_tests/test_w_fluxanl.py tool_tests/test_w_trace.py
description:
Added some unit tests for command line tools - these require a west.h5 output file in the tool_tests directory to work properly
changeset: 101:67495d11610c
parent: 100:e23601fbc913
parent: 99:8dfcf0b2b039
user: Matt Zwier <[email protected]>
date: Mon Apr 15 14:47:49 2013 -0400
description:
Merging
changeset: 100:e23601fbc913
parent: 98:41547e70fea2
user: Matt Zwier <[email protected]>
date: Mon Apr 15 14:47:18 2013 -0400
files: w_assign.py w_kinavg.py w_kinetics.py westpa/_rc.py westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx westpa/kinetics/matrates.py
description:
Added --no-compression option to w_kinetics to reduce I/O costs for w_kinavg.
Removed multiprocessing debug messages from default logging configs. Made
consistency warnings for matrix kinetics actual Python warnings.
changeset: 99:8dfcf0b2b039
user: Nick Rego <[email protected]>
date: Fri Apr 12 11:58:54 2013 -0400
files: w_trace.py
description:
W_trace works with h5io
changeset: 98:41547e70fea2
user: Matt Zwier <[email protected]>
date: Wed Apr 10 14:08:12 2013 -0400
files: w_kinavg.py westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx
description:
Fixed bug in kinetics tracing that gave completely wrong results for >2 states
changeset: 97:49097dcf063a
parent: 96:78d66a3e3f6e
parent: 91:f750d6047ae1
user: Matt Zwier <[email protected]>
date: Tue Apr 09 22:31:49 2013 -0400
files: w_assign.py
description:
Merging f750d6047ae1 and 78d66a3e3f6e
changeset: 96:78d66a3e3f6e
user: Matt Zwier <[email protected]>
date: Tue Apr 09 22:20:59 2013 -0400
files: mclib/__init__.py mclib/_mclib.c mclib/_mclib.pyx w_kinavg.py westpa/h5io.py westpa/kinetics/matrates.py
description:
Working parallel rate CI estimation for the matrix case.
changeset: 95:4972b298a26b
user: Matt Zwier <[email protected]>
date: Fri Apr 05 11:32:26 2013 -0400
files: mclib/__init__.py w_assign.py w_kinavg.py w_kinetics.py westpa/h5io.py westpa/kinetics/__init__.py westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx westtools/tool_classes/core.py westtools/tool_classes/data_reader.py westtools/tool_classes/iter_range.py
description:
Working parallel rate averaging for the tracing method.
changeset: 94:0d44069b92d7
user: Matt Zwier <[email protected]>
date: Thu Apr 04 11:20:15 2013 -0400
files: w_kinavg.py w_kinetics.py w_kinmat.py w_kintrace.py westtools/tool_classes/__init__.py westtools/tool_classes/core.py
description:
Migrated w_kinmat and w_kintrace into subcommands under w_kinetics. Improved
subcommand support in westtools.tool_classes
changeset: 93:90719ba344af
user: Matt Zwier <[email protected]>
date: Wed Mar 27 17:59:57 2013 -0400
files: w_assign.py w_kinavg.py w_kinetics.py w_kinmat.py w_kintrace.py w_pdist.py westpa/binning/__init__.py westpa/binning/_assign.c westpa/binning/_assign.pyx westpa/h5io.py westpa/kinetics/__init__.py westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx westpa/kinetics/matrates.py westtools/tool_classes/data_reader.py
description:
Reworked w_assign to work in parallel and with same dsspec mechanism as
w_pdist. Split w_kinetics into w_kintrace (tracing analyses) and w_kinmat
(matrix analyses). w_kinavg is broken at the moment.
changeset: 92:c157e83620aa
parent: 88:2d9498468184
user: Matt Zwier <[email protected]>
date: Wed Mar 27 14:40:21 2013 -0400
files: plothist.py w_pcpdist.py w_pdist.py westpa/h5io.py westtools/__init__.py westtools/tool_classes/__init__.py westtools/tool_classes/core.py westtools/tool_classes/data_reader.py westtools/tool_classes/hdf5_storage.py westtools/tool_classes/iter_range.py westtools/tool_classes/selected_segs.py westtools/tool_classes/stats.py
description:
Generalized handling of subcommands, synthetic datasets. Improved help.
changeset: 91:f750d6047ae1
user: Nick Rego <[email protected]>
date: Tue Apr 02 18:16:52 2013 -0400
files: tests/testwtools.py w_assign.py
description:
some more unit tests for w_kinetics
changeset: 90:b6c75ce796df
user: Nick Rego <[email protected]>
date: Wed Mar 27 20:09:32 2013 -0400
files: tests/testwtools.py w_assign.py
description:
w_assign sets number of workers to 1 if n_workers is 0 (possible for zeromq work manager to have a delay in counting workers on startup)
changeset: 89:7656029b3539
user: Nick Rego <[email protected]>
date: Tue Mar 26 12:24:55 2013 -0400
files: tests/testwtools.py
description:
small change to w_assign unit tests (to account for directly using n_workers attribute of work managers)
changeset: 88:2d9498468184
user: Matt Zwier <[email protected]>
date: Tue Mar 26 12:01:19 2013 -0400
files: w_assign.py westpa/binning/_assign.c westpa/binning/_assign.pyx
description:
Fixed indexing bug in _assign.pyx
changeset: 87:a0ddb9df7011
user: Matt Zwier <[email protected]>
date: Tue Mar 26 11:41:28 2013 -0400
files: w_assign.py
description:
Modified w_assign to use plain n_workers attribute from work manager (now that SerialWorkManager specifies that attribute).
changeset: 86:705ed2b01997
parent: 85:dfc890b9f5c3
parent: 82:3568b062d973
user: Matt Zwier <[email protected]>
date: Tue Mar 26 11:34:51 2013 -0400
files: w_assign.py westpa/binning/_assign.c westpa/kinetics/_kinetics.c
description:
Merging 3568b062d973 and dfc890b9f5c3
changeset: 85:dfc890b9f5c3
user: Matt Zwier <[email protected]>
date: Mon Mar 25 14:53:12 2013 -0400
files: fasthist/__init__.py plothist.py w_assign.py w_fluxanl.py w_kinavg.py w_kinetics.py w_pcpdist.py w_pdist.py westpa/h5io.py westpa/textio.py westtools/__init__.py westtools/h5io.py westtools/textio.py westtools/tool_classes/core.py westtools/tool_classes/iter_range.py
description:
Moved h5io and textio from westtools/ to westpa/ to avoid an import conflict
with data_manager.py. Fixed multiple problems with plothist, particularly for
3-D cases. Made DSSpecs (w_pdist) picklable and parallelized w_pdist. w_assign
now accepts a function that returns a bin-to-state mapping in the same rough
format as the YAML file would deliver.
changeset: 84:2a5234adbc06
user: Matt Zwier <[email protected]>
date: Wed Mar 20 12:43:50 2013 -0400
files: w_pdist.py
description:
Working w_pdist for extracting probability distributions from arbitrary data sets.
Needs to be optimized for memory use.
changeset: 83:9f6cd0642b97
parent: 77:98ed9daf55e2
user: Matt Zwier <[email protected]>
date: Sat Mar 16 11:48:57 2013 -0400
files: w_pdist.py
description:
Copyied w_pcpdist.py to start w_pdist.py
changeset: 82:3568b062d973
user: Nick Rego <[email protected]>
date: Tue Mar 26 11:05:47 2013 -0400
files: tests/testwtools.py westpa/binning/_assign.c westpa/binning/_assign.pyx
description:
w_assign parallelization and some unit tests
changeset: 81:c5a0cc01860d
user: Nick Rego <[email protected]>
date: Mon Mar 25 15:09:19 2013 -0400
files: tests/testwtools.py w_assign.py westpa/binning/_assign.c westpa/binning/_assign.pyx
description:
w_assign should support parallelization (for now - for all work managers but zmq); most unit tests for w_assign set up
changeset: 80:b2055a4060bc
user: Nick Rego <[email protected]>
date: Wed Mar 20 12:12:36 2013 -0400
files: tests/testwtools.py w_assign.py westpa/binning/_assign.c westpa/binning/_assign.pyx
description:
added some test cases for west_tools (w_assign); assign_and_label method in _assign.pyx modified to allow slicing over a subset of the segments
changeset: 79:ed1474805f1b
user: Nick Rego <[email protected]>
date: Tue Mar 19 15:51:29 2013 -0400
files: tests/testwtools.py w_assign.py
description:
w_assign works if you don't specify macrostates (but subsequent analysis may require macrostates)
changeset: 78:f0f1f9caf6a0
user: Nick Rego <[email protected]>
date: Tue Mar 19 11:06:03 2013 -0400
files: tests/testwtools.py
description:
created unit test script for west_tools
changeset: 77:98ed9daf55e2
parent: 76:76a57ac6fb2a
parent: 74:c326331f3b0d
user: Matt Zwier <[email protected]>
date: Thu Mar 14 16:23:07 2013 -0400
description:
Merging 76a57ac6fb2a
changeset: 76:76a57ac6fb2a
parent: 75:3b0dba86acbc
parent: 73:13c5da215394
user: Matt Zwier <[email protected]>
date: Thu Mar 14 16:21:49 2013 -0400
description:
Merging c326331f3b0d
changeset: 75:3b0dba86acbc
parent: 71:034dfa681051
user: Matt Zwier <[email protected]>
date: Thu Mar 14 16:20:08 2013 -0400
files: w_assign.py westpa/binning/_assign.c westpa/binning/_assign.pyx
description:
Allowed w_assign to run with 0, 2, or more macrostates. Resolves #30.
changeset: 74:c326331f3b0d
user: Nick Rego <[email protected]>
date: Wed Mar 13 14:34:49 2013 -0400
files: plothist.py
description:
plothist: can add a plot title when plotting in 'evolution' mode
changeset: 73:13c5da215394
parent: 72:dde3e236e443
parent: 71:034dfa681051
user: Nick Rego <[email protected]>
date: Tue Mar 12 12:45:35 2013 -0400
description:
merge before push
changeset: 72:dde3e236e443
parent: 70:c1409c69065f
user: Nick Rego <[email protected]>
date: Tue Mar 12 12:33:02 2013 -0400
files: plothist.py
description:
Plothist plot options - title not mutually exclusive with log transformation, etc
changeset: 71:034dfa681051
user: Matt Zwier <[email protected]>
date: Thu Mar 07 17:09:16 2013 -0500
files: w_assign.py w_kinavg.py w_kinetics.py westpa/kinetics/__init__.py westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx
description:
Using more stable eigenvalue routine for kinetics analysis.
changeset: 70:c1409c69065f
parent: 69:6c019a08d1ef
parent: 51:753c07d3bfc7
user: Matt Zwier <[email protected]>
date: Tue Mar 05 17:10:49 2013 -0500
description:
Merging in 753c07d3bfc7
changeset: 69:6c019a08d1ef
user: Matt Zwier <[email protected]>
date: Tue Mar 05 16:57:32 2013 -0500
files: w_kinavg.py westpa/kinetics/__init__.py westtools/tool_classes/__init__.py westtools/tool_classes/core.py
description:
New kinetics analysis working for equilibrium simulations
changeset: 68:e6dc5079bb30
user: Matt Zwier <[email protected]>
date: Tue Mar 05 12:54:23 2013 -0500
files: w_kinavg.py
description:
Working kinetic averaging without error bars
changeset: 67:7ecbf51771b9
user: Matt Zwier <[email protected]>
date: Tue Mar 05 12:43:06 2013 -0500
files: w_kinetics.py westpa/kinetics/__init__.py westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx
description:
One-pass matrix and tracing kinetics analysis largely complete
changeset: 66:4cf9907ae7dc
user: Matt Zwier <[email protected]>
date: Mon Mar 04 17:49:34 2013 -0500
files: w_kinetics.py westpa/_rc.py westpa/binning/__init__.py westpa/binning/_assign.c westpa/kinetics/__init__.py westpa/kinetics/_kinetics.c westpa/kinetics/_kinetics.pyx westtools/h5io.py westtools/tool_classes/iter_range.py
description:
Prototype state-to-state flux tracer in-line with matrix calculations
changeset: 65:8dd6779a2796
user: Matt Zwier <[email protected]>
date: Mon Mar 04 17:48:51 2013 -0500
files: plothist.py
description:
Added plot title option to plothist.py
changeset: 64:090b26218897
parent: 63:70f6a863ae66
parent: 50:d15db6db5f57
user: Matt Zwier <[email protected]>
date: Thu Feb 28 14:57:03 2013 -0500
description:
Merged upstream (d15db6db5f57)
changeset: 63:70f6a863ae66
user: Matt Zwier <[email protected]>
date: Thu Feb 28 14:55:10 2013 -0500
files: tests/testbinning.py w_assign.py w_kinetics.py westpa/binning/_assign.pyx westpa/kinetics/_kinetics.pyx
description:
Kinetics assignment prototype complete. westpa.assign now uses the buffer
interface instead of the numpy interface where possible.
changeset: 62:98acd458d784
user: Matt Zwier <[email protected]>
date: Wed Feb 27 16:53:33 2013 -0500
files: w_assign.py w_kinetics.py
description:
Updated working kinetics analysis code to relocated binning extension
changeset: 61:ff1429b74af1
parent: 60:0ad23d2371fb
parent: 48:cd0316c3e174
user: Matt Zwier <[email protected]>
date: Wed Feb 27 16:35:22 2013 -0500
description:
Merging in dcf0bdd3f498 (transplant of binning/assign extensions)
changeset: 60:0ad23d2371fb
parent: 59:f2d523404ae1
parent: 34:f4c809a9d9c4
user: Matt Zwier <[email protected]>
date: Wed Feb 27 15:46:46 2013 -0500
files: examples/ex_graphtest.py westtools/tool_classes/data_reader.py westtools/tool_classes/iter_range.py
description:
Merged in f4c809a9d9c4
changeset: 59:f2d523404ae1
user: Matt Zwier <[email protected]>
date: Wed Feb 27 15:39:48 2013 -0500
files: w_assign.py w_kinetics.py
description:
Updated assignment code and prototype flux accumulator.
changeset: 58:ab67b56af11c
user: Matt Zwier <[email protected]>
date: Wed Feb 27 15:37:44 2013 -0500
files: westtools/h5io.py
description:
Fixed occasional crash due to dtype oddity.
changeset: 57:4ea3af8a990c
user: Matt Zwier <[email protected]>
date: Mon Feb 25 16:24:30 2013 -0500
files: w_kinetics.py
description:
DMZ algorithm refinements
changeset: 56:f4413905da7c
user: Matt Zwier <[email protected]>
date: Mon Feb 25 12:49:49 2013 -0500
files: w_kinetics.py
description:
First pass at DMZ algorithm
changeset: 55:19b32b4ce8cf
user: Matt Zwier <[email protected]>
date: Thu Feb 21 16:45:36 2013 -0500
files: w_kinetics.py
description:
w_kinetics gets an overall flux and event durations, but reverse rates could be trouble
changeset: 54:228ed6c610d7
user: Matt Zwier <[email protected]>
date: Thu Feb 21 16:18:01 2013 -0500
files: w_assign.py w_kinetics.py
description:
Skeleton of required bits of w_kinetics
changeset: 53:61fb1f670cb3
user: Matt Zwier <[email protected]>
date: Thu Feb 21 13:57:37 2013 -0500
files: ex_fluxanl_plot.py ex_fpp.py ex_graphtest.py examples/ex_fluxanl_plot.py examples/ex_graphtest.py functional_tests/t_mclib.py functional_tests/t_treewalker.py t_mclib.py t_treewalker.py w_assign.py w_kinetics.py w_pdist.py westtools/h5io.py westtools/tool_classes/data_reader.py westtools/tool_classes/iter_range.py
description:
Created w_assign for generalized assignments. Axed crazy generalized dataset
access in data_reader.py. Moved some things about.
changeset: 52:985aeece1197
parent: 33:beefda169ee2
user: Matt Zwier <[email protected]>
date: Fri Feb 15 16:39:43 2013 -0500
files: w_kinetics.py westtools/h5io.py
description:
Working commit for kinetics analysis
changeset: 51:753c07d3bfc7
user: Nick Rego <[email protected]>
date: Fri Mar 01 14:33:26 2013 -0500
files: w_trace.py
description:
Bug-fix (#14): w_trace should now work
changeset: 50:d15db6db5f57
user: joshua.adelman <[email protected]>
date: Thu Feb 28 14:26:30 2013 -0500
files: westpa/kinetics/rate_averaging.py
description:
Fixed bug in rate_averaging for recycling simulations. Resolves issue #21
changeset: 49:e175ad537dfe
user: joshua.adelman <[email protected]>
date: Thu Feb 28 13:26:27 2013 -0500
files: fasthist/_fasthist.c mclib/_mclib.c setup.py trajtree/_trajtree.c westpa/binning/_assign.c westpa/kinetics/_kinetics.c westtools/trajlib/__init__.py
description:
Updated setup.py to compile extensions from source if cython is not available and started tracking .c files in repo. Resolves WESTPA issue #18
changeset: 48:cd0316c3e174
user: Matt Zwier <[email protected]>
date: Wed Feb 27 16:23:54 2013 -0500
files: setup.py tests/testbinning.py westpa/kinetics/rate_averaging.py westtools/tool_classes/binning.py
description:
Moved binning and kinetics extensions to west_tools
changeset: 47:4a6ecad323c0
parent: 34:f4c809a9d9c4
parent: 46:dcf0bdd3f498
user: Matt Zwier <[email protected]>
date: Wed Feb 27 16:08:30 2013 -0500
description:
Merging dcf0bdd3f498 (transplant of west.binning/west.assign history)
changeset: 46:dcf0bdd3f498
user: Matt Zwier <[email protected]>
date: Wed Feb 27 15:58:26 2013 -0500
files: src/west/binning/__init__.py src/west/binning/_assign.pyx src/west/binning/assign.py src/west/binning/bins.py src/west/kinetics/__init__.py src/west/kinetics/_kinetics.pyx src/west/kinetics/rate_averaging.py westpa/binning/__init__.py westpa/binning/_assign.pyx westpa/binning/assign.py westpa/binning/bins.py westpa/kinetics/__init__.py westpa/kinetics/_kinetics.pyx westpa/kinetics/rate_averaging.py
description:
Relocated files prior to import into west_tools
changeset: 45:a983fb052832
user: Matt Zwier <[email protected]>
date: Wed Feb 27 15:32:46 2013 -0500
files: src/west/kinetics/rate_averaging.py
description:
Changed all west.rc references to westpa.rc
changeset: 44:2c6d6eac838a
parent: 42:038e769b238c
parent: 43:57e6d4facf4c
user: Matt Zwier <[email protected]>
date: Wed Feb 27 15:15:10 2013 -0500
description:
Merging b90ad753864f and 2a88258c58db
changeset: 43:57e6d4facf4c
parent: 41:261add038b66
user: Matt Zwier <[email protected]>
date: Wed Feb 27 15:04:08 2013 -0500
files: src/west/binning/assign.py